The Generic Genome Browser (GBrowse) is a genome [[Visualization|viewer]] and is [[GMOD]]'s most popular [[GMOD Components|component]]. For a demo of its features, see [http://wormbase.org/db/gb2/gbrowse/c_elegans/ WormBase], [http://flybase.org/cgi-bin/gbrowse/dmel FlyBase], or [http://projects.tcag.ca/cgi-bin/duplication/dupbrowse/human_b35 Human Genome Segmental Duplication Database] and [[GMOD_Users|others]].

+

|dev=active

−

+

|support=active

−

==Description==

+

|type=Genome Visualization & Editing

−

[[image:gbrowse_screenshot1.gif|right|thumb|350px|GBrowse running on [http://hapmap.org/downloads/index.html HapMap.org] [[Media:gbrowse_screenshot1.gif|Click to view at full resolution]]]]

+

|platform=web

−

+

|about=GBrowse is a combination of database and interactive web pages for manipulating and displaying annotations on genomes. Features include:

−

GBrowse is a combination of database and interactive web pages for manipulating and displaying annotations on genomes. Some of its features include:

Note that the information on this page refers to GBrowse 2; GBrowse 1.x is recommended only for applications where legacy browser support is required and a single database is used.

−

+

|open source=Yes

−

'''GBrowse 1.X''' (currently 1.70) is the older series that has been in use since 2002. It is recommended for applications which use a single database only and which must support legacy browsers.

+

|licence=GPL2, Artistic License

−

+

|input=GFF3, GFF2

−

'''GBrowse 2.0''' is a rewrite of the original GBrowse to add dynamic updating via AJAX and a smoother user experience. In addition, it provides administrators with the ability to attach a different genome database to each GBrowse track, making it much easier to manage and update tracks. It also provides a distributed backend system of "slave" renderers, allowing each track to be rendered in parallel on a different machine and significantly increasing performance. GBrowse 2.0 is considered stable,but does not have full internationalization support. In addition, there may be issues with older browsers that do not support newer JavaScript features.

+

|language=Perl

−

+

|release date=2001/01/01

−

==Installation==

+

|logo=GBrowseLogo.png

−

+

|screenshot=[[image:GBrowse_screenshot1.png|none|thumb|500px|GBrowse running on [http://hapmap.ncbi.nlm.nih.gov/downloads/index.html HapMap.org] [[Media:GBrowse_screenshot1.png|Click to view at full resolution]]]]

−

GBrowse is [[Glossary#Perl|Perl]]-based. It can be installed using the standard Perl module build procedure, or automated using a network-based install script. In order to use the net installer, you will need to have Perl 5.8.6 or higher and the Apache web server installed. See the step-by-step instructions below for detailed instructions:

: Demonstrates setting up, configuring and using [[GBrowse]] with some sample data. GBrowse is provided on an Amazon Machine Image; see [[Cloud|GMOD in the Cloud]] for more information on getting a GMOD AMI.

: Set up and run [[GBrowse]] with sample data. It provides a VMware image to work on, and relies heavily on the {{GBrowseAdminTutorialLink|GBrowse Administration Tutorial}}.

+

; {{GBrowseAdminTutorialLink|GBrowse Administration Tutorial}}

+

: Step by step guide on how to configure and load data into [[GBrowse]]. Administration tutorials are available for both the {{GBrowseAdminTutorialLink|current version}}, and the earlier {{GBrowse1AdminTutorialLink|1.x versions}}.

: Instructions on how to visualize [[next generation sequencing]] data in GBrowse using [http://samtools.sourceforge.net SAMtools]. The tutorial includes a starting VMware image, and uses the example data that comes with SAMtools.

+

; [http://youtu.be/jxA6VMN97Y8 GBrowse video tutorial]

+

: Produced by [http://eupathdb.org EuPathDB]; please direct praise and thanks to them!

: A Flash based tutorial on using GBrowse. Provided by [http://www.openhelix.com OpenHelix]. Tutorial includes slides, handouts and exercises. NB: this tutorial is for [[GBrowse 1.x]]

+

|req=GBrowse is [[Glossary#Perl|Perl]]-based and the GBrowse 2.x modules are [http://search.cpan.org/dist/GBrowse/ hosted on CPAN]. GBrowse can be installed using the standard Perl module build procedure, or automated using a network-based install script. In order to use the net installer, you will need to have Perl 5.8.6 or higher and the Apache web server installed.

Since these are in Perl POD format these files may contain formatting code when viewed in a Web browser.

+

GBrowse 2.x pod documents can also be viewed online at CPAN:

−

==Downloads==

+

* {{GBrowse_pod|FAQ}}

+

* {{GBrowse_pod|INSTALL}}

+

* {{GBrowse_pod|INSTALL.MacOSX}}

+

* {{GBrowse_pod|README-chado}}

+

* {{GBrowse_pod|README-gff-files}} (see also [[GFF]])

+

* {{GBrowse_pod|README-lucegene}}

+

* {{GBrowse_pod|BIOSQL_ADAPTER_HOWTO}}

+

* {{GBrowse_pod|GENBANK_HOWTO}}

+

* {{GBrowse_pod|PLUGINS_HOWTO}}

+

* {{GBrowse_pod|DAS_HOWTO}}

+

* {{GBrowse_pod|MAKE_IMAGES_HOWTO}}

+

* {{GBrowse_pod|GBROWSE_IMG}}

+

* {{GBrowse_pod|ORACLE_AND_POSTGRESQL}}

−

=== Source Code Download (tar.gz file) ===

+

===Installation===

−

Download the source from the [http://sourceforge.net/project/showfiles.php?group_id=27707 SourceForge download page].

+

* [[GBrowse_2.0_Install_HOWTO|GBrowse 2.x installation guide]]

+

* [[GBrowse 2.0 Install HOWTO/Advanced|Advanced]]

+

* [[GBrowse 2.0 Install Paths|Install Paths]]

−

=== Net-based Installer Script ===

+

===Configuration===

−

The net installer script, located at {{SF_SVN|Generic-Genome-Browser/trunk/bin/gbrowse_netinstall.pl|the GBrowse SVN repository}} will automatically download and install GBrowse and its Perl libraries for you. See [[#Installation|Installation]] for details on using this script.

There are often new features and bug fixes in the current development version which have not yet been released. To get the latest version, please use [[Subversion]] (SVN). The recommended branch to use is ''trunk'', which is usually stable:

The [[:Image:GBrowseLogo.png|GBrowse logo]] was created by [mailto:alexisnb1@yahoo.com Alex Read], a participant in the [[Spring 2010 Logo Program]], while a design student at [http://www.linn-benton.edu Linn-Benton Community College].

+

−

==References==

+

There are many useful POD documents included with the distribution. These are converted to HTML files when you install the package, and can be found in /gbrowse/docs/pod.

|logo info=The [[:File:GBrowseLogo.png|GBrowse logo]] was created by [mailto:alexisnb1@yahoo.com Alex Read], a participant in the [[Spring 2010 Logo Program]], while a design student at [http://www.linnbenton.edu Linn-Benton Community College].

+

|see also=[[JBrowse]], the successor to GBrowse, built with JavaScript for a faster, more interactive user experience; and [[WebGBrowse]], a tool for configuring GBrowse.

Using GBrowse

System Requirements

GBrowse is Perl-based and the GBrowse 2.x modules are hosted on CPAN. GBrowse can be installed using the standard Perl module build procedure, or automated using a network-based install script. In order to use the net installer, you will need to have Perl 5.8.6 or higher and the Apache web server installed.

Note that the information on this page refers to GBrowse 2; GBrowse 1.x is recommended only for applications where legacy browser support is required and a single database is used.is required and a single database is used. +